< SIGs | NeuroFedora
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There is a good amount of overlap with other SIGs and Spins and some categories of NeuroFedora can be seen as BigData, Fedora-Medical, ML, Octave and SciTech in general. | There is a good amount of overlap with other SIGs and Spins and some categories of NeuroFedora can be seen as BigData, Fedora-Medical, ML, Octave and SciTech in general. | ||
Please add software that needs to be packaged to the appropriate table with the status "needs packaging". If a package is in a COPR repository, a status of "COPR" can be used. Once a package is in review, the status should be "In review", and of course, once a package is in the repositories, the final status would be "Packaged". | |||
Please feel free to reorganise the tables as required. | |||
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! Package !! Summary !! Status !! Comment | ! Package !! Summary !! Status !! Comment | ||
|- | |- | ||
| | | {{FpPackage| }} || || Packaged || | ||
|- | |- | ||
|} | |} | ||
== Packages for | == Packages for Image analysis == | ||
{| class="wikitable" | {| class="wikitable" | ||
|- | |- | ||
! Package !! Summary !! Status !! Comment | ! Package !! Summary !! Status !! Comment | ||
|- | |- | ||
| | | {{FpPackage|ctk }} || The CTK core library for Image analysis || Packaged || | ||
|- | |||
| {{FpPackage|dcm2niix }} || Conver neuroimaging data from NIFTI format to DICOM || Packaged || | |||
|- | |||
| {{FpPackage|isis }} || Framework to access a large variety of image libraries|| Needs import || | |||
|- | |- | ||
| | | {{FpPackage| libminc }} || Library to work with the MINC file format || Packaged || | ||
|- | |||
| {{FpPackage|python-nibabel }} || Python package to access a cacophony of neuro-imaging file formats|| Packaged || | |||
|- | |||
| {{FpPackage|python-pydicom }} || Read, modify, and write DICOM files with Python|| Packaged || | |||
|- | |||
| {{FpPackage|rubygem-nifti }} || Pure-ruby library for handling NIfTI data in Ruby|| Packaged || | |||
|- | |- | ||
|} | |} | ||
== Packages for | |||
== Packages for Data Analysis == | |||
{| class="wikitable" | {| class="wikitable" | ||
|- | |- | ||
! Package !! Summary !! Status !! Comment | ! Package !! Summary !! Status !! Comment | ||
|- | |- | ||
| | | {{FpPackage|python-mne }} || Magnetoencephalography (MEG) and Electroencephalography (EEG) data analysis || Packaged || | ||
|- | |- | ||
| | | {{FpPackage|python-pyactivetwo }} ||Python library for reading signal from BioSemi ActiveTwo EEG device || Packaged || | ||
|- | |- | ||
|} | |} | ||
== Packages for Modeling of neural systems == | == Packages for Modeling of neural systems == | ||
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! Package !! Summary !! Status !! Comment | ! Package !! Summary !! Status !! Comment | ||
|- | |- | ||
| | | [http://nest-simulator.org NEST neural simulator] || The neural simulation tool|| In review, needs work [[rhbug:1273579| 1273579]] || | ||
|- | |- | ||
| | | [http://briansimulator.org/ Brian] || The Brian spiking neural simulator || Needs packaging, dead review [[rhbug:1098754|1098754]] || | ||
|- | |||
| [https://github.com/NeuralEnsemble/PyNN PyNN] || A Python package for simulator independent specification of neuronal network models|| Review ready, needs deps [[rhbug:1150105| 1150105]]|| | |||
|- | |||
| [https://www.neuron.yale.edu/neuron/ The NEURON simulator] || Empirically based simulations of neurons and networks of neurons|| Needs packaging, dead review [[rhbug:1249094|1249094]]|| | |||
|- | |||
| {{FpPackage| }} || || Packaged || | |||
|- | |- | ||
|} | |} | ||
== | == Misc Libraries/Utilities == | ||
{| class="wikitable" | {| class="wikitable" | ||
|- | |- | ||
! Package !! Summary !! Status !! Comment | ! Package !! Summary !! Status !! Comment | ||
|- | |- | ||
| | | {{FpPackage|python-neo}} || Represent electrophysiology data in Python || Packaged || | ||
|- | |||
| {{FpPackage| DiffusionKurtosisFit }} || Reconstruct Diffusion Kurtosis tensor from Diffusion Weighted MRI || Packaged || | |||
|- | |||
| {{FpPackage|getdp }} || Finite element solver || Packaged || | |||
|- | |||
| {{FpPackage| gifticlib }} || Refernce IO implementation and tools of the GIFTI XML based file format for cortical surface data || Packaged || | |||
|- | |||
| {{FpPackage|nipy-data }} || Test data and brain templates for nipy|| Packaged || | |||
|- | |||
| {{FpPackage|openigtlink }} || Reference implementation of OpenIGTLink: a set of message formats and protocols used for data exchange over a local area network|| Packaged || | |||
|- | |||
| {{FpPackage|petpvc }} || Tools for partial volume correction (PVC) in positron emission tomography (PET)|| Packaged || | |||
|- | |||
| {{FpPackage|python-amico }} || Relationships backed by Redis|| Packaged || | |||
|- | |||
| {{FpPackage|python-baker }} || Easy, powerful access to Python functions from the command line|| Packaged || | |||
|- | |||
| {{FpPackage|python-citeproc-py }} || Citations and bibliography formatter|| Packaged || | |||
|- | |||
| {{FpPackage|python-gradunwarp }} || Gradient Unwarping|| Packaged || | |||
|- | |||
| {{FpPackage|python-h5io }} || Read and write simple Python objects using HDF5|| Packaged || | |||
|- | |- | ||
| | | {{FpPackage|python-interfile }} || Python module for read/write/parse interfile|| Packaged || | ||
|- | |||
| {{FpPackage|python-klusta }} || Spike detection and automatic clustering for spike sorting|| Packaged || | |||
|- | |- | ||
| {{FpPackage|python-lazyarray }} || A lazily-evaluated numerical array class|| Packaged || | |||
{| class | |||
|- | |- | ||
| {{FpPackage|python-moss }} || Assorted utilities for neuroimaging and cognitive science|| Packaged || | |||
|- | |- | ||
| | | {{FpPackage|python-nixio }} || Python bindings for NIX, the Neuroscience Exchange Format|| Packaged || | ||
|- | |- | ||
| | | {{FpPackage|python-pydotplus }} || Python interface to Graphviz's Dot language|| Packaged || | ||
|- | |- | ||
| | | {{FpPackage|python-PyLink }} || Universal communication interface using File-Like API|| Packaged || | ||
|- | |- | ||
| {{FpPackage|python-pyoptical }} || Pure Python interface to OptiCAL|| Packaged || | |||
|- | |- | ||
| | | {{FpPackage|python-pyriemann }} || Covariance matrices manipulaton and Biosignal classification|| Packaged || | ||
|- | |- | ||
| | | {{FpPackage|python-pyxid }} || Python library for interfacing with Cedrus XID and StimTracker devices|| Packaged || | ||
|- | |- | ||
| | | {{FpPackage|python-quantities }} || Support for physical quantities with units, based on numpy|| Packaged || | ||
|- | |- | ||
| {{FpPackage|python-simplewrap }} || Easy to use wrappers generator for C libraries based on ctypes|| Packaged || | |||
|- | |- | ||
| {{FpPackage|python- | | {{FpPackage| python-tabulate }} || Pretty-print tabular data in Python, a library and a command-line utility|| Packaged || | ||
|- | |- | ||
| | | {{FpPackage| python-transforms3d}} || 3 dimensional spatial transformations|| Packaged || | ||
|- | |- | ||
|} | |} |
Revision as of 23:12, 21 June 2018
There is a good amount of overlap with other SIGs and Spins and some categories of NeuroFedora can be seen as BigData, Fedora-Medical, ML, Octave and SciTech in general.
Please add software that needs to be packaged to the appropriate table with the status "needs packaging". If a package is in a COPR repository, a status of "COPR" can be used. Once a package is in review, the status should be "In review", and of course, once a package is in the repositories, the final status would be "Packaged".
Please feel free to reorganise the tables as required.
Packages for Distributed Computing
Package | Summary | Status | Comment |
---|---|---|---|
[1] | Packaged |
Packages for Image analysis
Package | Summary | Status | Comment |
---|---|---|---|
ctk | The CTK core library for Image analysis | Packaged | |
dcm2niix | Conver neuroimaging data from NIFTI format to DICOM | Packaged | |
isis | Framework to access a large variety of image libraries | Needs import | |
libminc libminc | Library to work with the MINC file format | Packaged | |
python-nibabel | Python package to access a cacophony of neuro-imaging file formats | Packaged | |
python-pydicom | Read, modify, and write DICOM files with Python | Packaged | |
rubygem-nifti | Pure-ruby library for handling NIfTI data in Ruby | Packaged |
Packages for Data Analysis
Package | Summary | Status | Comment |
---|---|---|---|
python-mne | Magnetoencephalography (MEG) and Electroencephalography (EEG) data analysis | Packaged | |
python-pyactivetwo | Python library for reading signal from BioSemi ActiveTwo EEG device | Packaged |
Packages for Modeling of neural systems
Package | Summary | Status | Comment |
---|---|---|---|
NEST neural simulator | The neural simulation tool | In review, needs work 1273579 | |
Brian | The Brian spiking neural simulator | Needs packaging, dead review 1098754 | |
PyNN | A Python package for simulator independent specification of neuronal network models | Review ready, needs deps 1150105 | |
The NEURON simulator | Empirically based simulations of neurons and networks of neurons | Needs packaging, dead review 1249094 | |
[2] | Packaged |
Misc Libraries/Utilities
Package | Summary | Status | Comment |
---|---|---|---|
python-neo | Represent electrophysiology data in Python | Packaged | |
DiffusionKurtosisFit DiffusionKurtosisFit | Reconstruct Diffusion Kurtosis tensor from Diffusion Weighted MRI | Packaged | |
getdp | Finite element solver | Packaged | |
gifticlib gifticlib | Refernce IO implementation and tools of the GIFTI XML based file format for cortical surface data | Packaged | |
nipy-data | Test data and brain templates for nipy | Packaged | |
openigtlink | Reference implementation of OpenIGTLink: a set of message formats and protocols used for data exchange over a local area network | Packaged | |
petpvc | Tools for partial volume correction (PVC) in positron emission tomography (PET) | Packaged | |
python-amico | Relationships backed by Redis | Packaged | |
python-baker | Easy, powerful access to Python functions from the command line | Packaged | |
python-citeproc-py | Citations and bibliography formatter | Packaged | |
python-gradunwarp | Gradient Unwarping | Packaged | |
python-h5io | Read and write simple Python objects using HDF5 | Packaged | |
python-interfile | Python module for read/write/parse interfile | Packaged | |
python-klusta | Spike detection and automatic clustering for spike sorting | Packaged | |
python-lazyarray | A lazily-evaluated numerical array class | Packaged | |
python-moss | Assorted utilities for neuroimaging and cognitive science | Packaged | |
python-nixio | Python bindings for NIX, the Neuroscience Exchange Format | Packaged | |
python-pydotplus | Python interface to Graphviz's Dot language | Packaged | |
python-PyLink | Universal communication interface using File-Like API | Packaged | |
python-pyoptical | Pure Python interface to OptiCAL | Packaged | |
python-pyriemann | Covariance matrices manipulaton and Biosignal classification | Packaged | |
python-pyxid | Python library for interfacing with Cedrus XID and StimTracker devices | Packaged | |
python-quantities | Support for physical quantities with units, based on numpy | Packaged | |
python-simplewrap | Easy to use wrappers generator for C libraries based on ctypes | Packaged | |
python-tabulate python-tabulate | Pretty-print tabular data in Python, a library and a command-line utility | Packaged | |
python-transforms3d python-transforms3d | 3 dimensional spatial transformations | Packaged |